[Snyk] Security upgrade python from 3.13.2-slim-bookworm to 3.14.0rc1-slim-bookworm - #14
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[Snyk] Security upgrade python from 3.13.2-slim-bookworm to 3.14.0rc1-slim-bookworm#14jcschaff wants to merge 1 commit into
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The following vulnerabilities are fixed with an upgrade: - https://snyk.io/vuln/SNYK-DEBIAN12-GNUTLS28-10690985 - https://snyk.io/vuln/SNYK-DEBIAN12-GNUTLS28-10690987 - https://snyk.io/vuln/SNYK-DEBIAN12-GNUTLS28-10690990 - https://snyk.io/vuln/SNYK-DEBIAN12-GNUTLS28-10690993 - https://snyk.io/vuln/SNYK-DEBIAN12-SYSTEMD-10264074
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…eview biosimulations#14 (worker pod disk leak) -- wrap biosim_service.run_biosim_sim in try/finally inside submit_biosim_run_activity so local_omex_path is always removed, even when submit raises (HTTP 5xx, network, auth). The os.remove is itself wrapped in try/except OSError so a missing-file race during cleanup is non-fatal. biosimulations#5 (FAILED-row cache pollution) -- gate insert_biosimulator_workflow_run in poll_biosim_run_activity on `simulation_run.status == SUCCEEDED`. Non-SUCCEEDED runs still return a fully-populated (un-saved) BiosimulatorWorkflowRun so OmexSimWorkflow can surface the FAILED state -- the workflow does not consult database_id. Eliminates unbounded BiosimSims growth on failing inputs and removes the cache-lookup ordering hazard (cached_runs[0] could otherwise be a FAILED row hiding a later SUCCEEDED one). biosimulations#10 (missing Mongo indexes) -- add an ensure_indexes() method to all three Mongo DB services (default no-op on the abstract base; Mongo impls override). Called from init_standalone() and from each test fixture so production and tests share the same shape. Indexes: BiosimSimulationRuns: processing_id, run_id (unique) BiosimSims: (file_hash_md5, image_digest, cache_buster) compound + biosim_run.id BiosimOmex: file_hash_md5 (non-unique; the check-then-insert callers don't handle DuplicateKeyError, so uniqueness stays logical). #2 (status 404 after workflow history eviction) -- restructure GET /simulations/{processing_id}: don't 404 when the workflow query raises. Try the SimulationRunRecord DB fallback; only 404 if both sources are empty. A new _conglomerate_status_from_records helper builds ConglomerateStatus from persisted records when the workflow is gone (mapping CREATED/SUCCEEDED/FAILED back to processing/success/failure). Tests: 3 new router tests cover the workflow-not-found-with-DB-fallback path, the both-empty 404, and the hybrid enrichment-from-DB path. Existing test_get_simulation_status_not_found still passes (no records -> 404). Full -m "not integration" gate: 83 passed, 1 failed (the pre-existing test_slurm_service env failure, unchanged). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Snyk has created this PR to fix 5 vulnerabilities in the dockerfile dependencies of this project.
Keeping your Docker base image up-to-date means you’ll benefit from security fixes in the latest version of your chosen image.
Snyk changed the following file(s):
Dockerfile-workerWe recommend upgrading to
python:3.14.0rc1-slim-bookworm, as this image has only 44 known vulnerabilities. To do this, merge this pull request, then verify your application still works as expected.Vulnerabilities that will be fixed with an upgrade:
SNYK-DEBIAN12-GNUTLS28-10690985
SNYK-DEBIAN12-GNUTLS28-10690987
SNYK-DEBIAN12-GNUTLS28-10690990
SNYK-DEBIAN12-GNUTLS28-10690993
SNYK-DEBIAN12-SYSTEMD-10264074
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